Famke Janssen was originally cast as Serleena, and even completed some of the filming, but was forced to drop out of the project due to a death in the family. Lara Flynn Boyle was then cast in her place.
The original ending of the film included a scene in which the World Trade Center towers opened up, releasing a swarm of UFOs into the air. Following the towers' destruction, the film's ending was changed. Unfortunately this meant the film had a short running time, so when it was shown in theaters it was packed with trailers and the short film The Chubbchubbs! to fill the gap.
The steering mechanism in the car when flying near the ending scene is a silver-colored DualShock, the controller used for Sony's Playstation and PS2 consoles. This leads to J's joke about a "Gameboy".
During a scene in MIB headquarters, two aliens in black bodysuits can be seen walking around on all fours with their limbs straight, bobbing their heads up and down. The two aliens are played by Osseus Labyrint, an interpretive dance duo who toured with the band Tool and appeared in the band's video for "Schism". During the video, they perform the same move.
The stickers on Scrad's/Charlie's fridge door: "LOSER" "MY OTHER CAR - IS A SKATEBOARD - ALTERNATIVE PRESS" "HARASSING ME ABOUT MY SMOKING MAY BE HAZARDOUS TO YOUR HEALTH" "Your Kid's An Honor Student - But You're A Moron" "The Truth is NOT out There!" "BARTHAT - *SUCKS* - TIGERMASK - ..." "NEW YORK - MAFIA" "Greetings from New York City" (on postcard showing a heist)
Jay's line on the "driver airbag" ("Actually it came with a black dude, but he kept getting pulled over.") was not written in the script as Will Smith improvised it at the time. The producers liked it so much it even made the theatrical trailer. The Director however was not happy, it was played over and over in the month of June prior to the films release, making the joke old and tired by the time people saw it in the movie.
In the final battle versus Serleena, J says, "I'm 'bout to lay the smackdown on your candy ass." This phrase was coined by Dwayne Johnson when he was a full-time professional wrestler known as The Rock.
The extra head attached to Johnny Knoxville's character is called a 'symbiote,' and was first developed in Men in Black: The Series. It is the only development of the animated series to be carried over into the movies.
The noise the neuralyzer makes when it flashes is the sound of a strobe flash reloading. Sound editor Skip Lievsay filtered/modified the sound through a Synclavier synthesizer to make it more high-tech.
Barry Sonnenfeld took issue with the producers wanting to focus on the love story between Agent J and Laura: "I learned on Wild Wild West that audiences didn't want to see Will Smith as the straight man. And until Tommy Lee Jones comes back into the movie, by definition Will's the straight man."
In an interview with Will Smith and Tommy Lee Jones, Smith said: "It was great working with Frank the Pug in the first film, but since we came back he's been acting like an a-hole." Jones then said, "Yeah, Frank's had a bit of an identity crisis since the neutering."
The train locker is a tribute to the gangster mystery Once Upon a Time in America, where a main character (Agent K, Noodles) returns after a span of time and tries to solve a long-ago mystery; notably, the train locker contains a vital clue to solving the mystery.
In the Hungarian-dubbed version Elizabeth (the Young Girl at the Post Office) lines were redubbed from "Twenty Rugrats stamps please" to "South Park stamps please" because South Park was better known than Rugrats in Hungary that time. In the German-dubbed version her lines were re-dubbed to "Pokémon stamps please" because Pokémon was better known at that time.
According to Agent K, it rains when Zarthans cry. Two scenes are shown where it rains: when Laura cries, and in K's memories where he is seen with Princess Laurana. This also explains the connection with Agent K, Princess Laurana and Laura.